CLARC v1.1.0 - Initial Release

New Features

Added capability to process Panaroo output (running using the --panaroo flag)
Previous version was based on Prokka annotations, and now CLARC is also compatible with pangenomes built with Bakta annotations (more annotation formats can be added upon request)
Added merge function to merge different CLARC runs from the same pangenome analysis, but using the linkage of different defined populations
Added CLARC condensed version of the original Roary/Panaroo output file containing the number of sequences, sequence length, etc. to the standard outputs. This is in addition to the binary presence absence file with zeros and ones, as it also contains information on the gene tags corresponding to each re-defined COG.
Added flag to suppress accessory outputs (--dif, --delete-intermediate-files)

You can install by cloning the github repository, or update an existing installation by updating your local folder with:

git pull origin main

Then go to your local CLARC directory:

cd ~/CLARC

and run this command:

pip install dist/CLARC-X.X.X.tar.gz

where X.X.X corresponds to the latest version number (in this case, 1.1.0).

Please report any issues you encounter and/or request features you'd like to see!